+Open data
-Basic information
Entry | Database: PDB / ID: 3v7e | ||||||
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Title | Crystal structure of YbxF bound to the SAM-I riboswitch aptamer | ||||||
Components |
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Keywords | RIBOSOMAL PROTEIN/RNA / RNA-protein complex / riboswitch / K-turn / L7Ae-like / A member of the L7Ae/L30e superfamily / Unknown function / K-turn motif / RIBOSOMAL PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Baird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R. | ||||||
Citation | Journal: Rna / Year: 2012 Title: YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. Authors: Baird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v7e.cif.gz | 187.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v7e.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 3v7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7e ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7e | HTTPS FTP |
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-Related structure data
Related structure data | 3v7qC 1sdsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 8398.870 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU01090, rplGB, ybaB, ybxF / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: P46350 #2: RNA chain | Mass: 40800.328 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase Source: (synth.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) |
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-Non-polymers , 4 types, 57 molecules
#3: Chemical | ChemComp-NCO / #4: Chemical | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 150 M RNA, 210 M YbxF, 10 mM MgCl2, 10 mM SAM, 40 mM KCl, 20 mM HEPES-KOH, 1 mM spermine, 1 mM cobalt hexammine, and 1 mM DTT, 100 mM potassium cacodylate pH 6.0, 200 mM MgCl2 and 25% (v/v) ...Details: 150 M RNA, 210 M YbxF, 10 mM MgCl2, 10 mM SAM, 40 mM KCl, 20 mM HEPES-KOH, 1 mM spermine, 1 mM cobalt hexammine, and 1 mM DTT, 100 mM potassium cacodylate pH 6.0, 200 mM MgCl2 and 25% (v/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2011 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 25202 / Num. obs: 22926 / Observed criterion σ(I): 116.2 / Redundancy: 4.3 % / Biso Wilson estimate: 121.2 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.46 / Num. unique all: 2244 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: M. jannaschii L7Ae protein (PDB ID 1SDS, chain A) Resolution: 2.8→29.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 74723.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.0533 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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